WD Live HD - NTFS drive files turned into Folders

I have a WD LIVE HD

Recently i upgraded from 1.6.15 to 1.6.43

yesterday i found out that lots of my files turned into Folders !!!
 many files from small JPGs to larg MKVs

i downgraded to 1.05.04 and turned off media library but that did not help.

Chkdsk under windows didn’t help

i can recover my files with recovery softwares under windows , but in a 2TB drive with hundred thousends of files ,

first i have to list all the files that converted into folders then recover them 1 by 1 and it will take so much time.

is there an easier way to fix and get back my files !?